The Batman Adventures, the comic book spin-off of Batman: The Animated Series. That's right, it's a comic book based on a cartoon based on a comic book, and a damn fine one. Rather than cashing in on the popularity of the show by turning out cheap stories or adapting episodes, this was a tie-in that really did justice to the source material. At its best, one could even argue that it was better than B:TAS.
The first Jaime Reyes Blue Beetle run was really well written other than the first few issues. The main complaint was the undignified death of former Blue Beetle Ted Kord in a completely different title (Jaime's own series gave Ted big props). It was cancelled due to low sales but hopefully enough people buying the back issues will bring it back.
And in 2011, Jaime returns as part of DC's big relaunch, keeping his costume and supporting cast.
Chase, a DC comic book from late '90s. The premise — a (mostly) normal woman solving metahuman-related crimes in the DC Universe — was ahead of its time. It had a complex main character, a solid cast, and great art, but it was ingloriously cancelled after only 10 issues — and the last issue was a crossover with DC One Million that was completely unrelated to the main story. Thankfully, DC had the decency to wrap up the unresolved plot threads in their 2000 annuals, and Chase herself later became a supporting character in Manhunter... which was also too good to last.
The Courageous Princess: A princess from an obscure kingdom who isn't particularly rich or beautiful has to rely on her wits and kindness to escape from a dragon and get home, and all because no prince would bother to rescue her. Toss in some Talking Animals and Wacky Wayside Tribes and you've got the makings of a great adventure.
Doctor Strange, despite being a Marvel character, doesn't get a lot of attention, which is a shame because the comics are pretty cool.
Grim Jack by John Ostrander & Tim Truman, Flint Henry, Tom Mandrake, etc. If it's good enough for Roger Zelazny (a big fan, wrote the foreword to the Graphic Novel) it's good enough for anybody.
Hawkeye and Mockingbird, though anything with either counts too. (well, except for Hawkeye's current series, written by Matt Fraction and number 1 at the trade sales charts.) This series in particular, written by a Promoted Fanboy, really shines though, and was unneedingly cancelled after its sixth issue when it only finished its first arc.
PkNA. one of the greatest Disney series ever. chances are, if you're thinking of Donald Duck, you're not thinking of this series. Hopefully, With Disney buying Marvel, the series will get a relaunch....
The Red Circle books DC put out in 2009-2010: Great takes on interesting characters and awesome stories!
Marvel's Runaways. The premise is good (and provides a subtle social commentary on how teens see their parents), the plot twists are surprising and well-foreshadowed, and the characters are likable and realistic.
Rork. Very obscure yet brilliant comics series with complex, well-written plot, likeable characters, truly epic vibe and jaw-dropping art. If you like dieselpunk, inteligent story, Crazy Awesome ideas and deep mysticism, it's comics for you.
The Sabrina the Teenage Witch manga-style comic by Tania del Rio. This could have been just a cheap gimmick by Archie Comics. Instead, Tania took the manga idea beyond the look: it had good characters, a detailed mythos, and an actual arc.
Star Fox - yes, the very one. It expands on the original game's backstory, introducing new characters, concepts, action sequences, occasional light-hearted humour and a small measure of romance, well-dosed for the game's genre.
Xenozoic Tales: A well drawn pulp themed post-apocalyptic story with dinosaurs and larger-than-life personalities. It even went on to spawn an arcade beat-em-up and cartoon series. Unfortunately, creator Mark Schultz never gave the main story a proper ending, and it seems no one else has picked up the torch.
Monica Rambeau AKA CaptainMarvel AKA Photon AKA Pulsar AKA Spectrum is a Marvel Comics character who gain the power to absorb, manipulate and turn into energy on the electromagnetic spectrum, and fly at the speed of light while in her energy form. She is one of the most powerful characters in the Marvel Universe. She was a member of the Avengers (the first black female member in fact) and even lead them for a while. But for some reason, few people have even heard of her.
Ultraduck, by mexican author Edgar Delgado who works at Marvel. While it may not be the most original tale ever, is still a charming tale of a young man trying to grow up to impress his crush, while becoming a cool superhero. It has really good artwork, with a nice feel of a superhero tale, and is pretty cool! Keep in mind i'm talking about the remake, which you can find on Comixology, not the original one, which is charming on his own amateur right, but the remake shows how much the author has improved over the years.